In regard to your 2024 Form 5329, only the amount from box 2 from a code JP 2025 Form 1099-R goes on line 1 of this From 5329 because only taxable amounts are potentially subject to an early-distribution penalty. However, the NIA gains distributed with a return of contribution before the due date of the tax return, including extensions, are an exception to the penalty, so line 2 of the 2024 Form 5329 should show with code 21 the same amount as is on line 1.
[Correction]
Because the excess contributions for 2021, 2022 and 2023 were not corrected until 2025, Part IV of your 2024 Form 5329 will still show the total of these excess contributions which are subject to penalty for 2024. Part IV of the 2025 Form 5329 will need to be prepared to eliminate the excesses carried into 2025 from 2024.
If you were under age 59½ at the time of these distributions or it has been less than 5 years since beginning of the year for which you first made a Roth IRA contribution, 2025 [correction, not 2024] Form 8606 Part III is required to make the distribution of the 2021, 2022, and 2023 excesses nontaxable. Even though they were excess contributions, they added to your basis in Roth IRA contributions which needs to be subtracted from the total of these distributions.
You didn't ask about Part IV of 2021, 2022 and 2023 Forms 5329. These should have been filed and, if were not filed, need to be filed and the penalties paid.
